Tag: kegg

Construction of a circRNA-miRNA-mRNA Regulated Pathway Involved in EGFR-TKI Lung Adenocarcinoma Resistance

1 Introduction Lung cancer is the leading cause of cancer-related deaths worldwide, with adenocarcinoma as the most common histological subtype.1 In recent years, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib (first generation) and osimertinib (third generation), have been widely used for lung adenocarcinoma patients harboring activated EGFR…

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KEGG REACTION: R06783

Entry R06783                      Reaction                                Name trans-cinnamate,NADH:oxygen oxidoreductase (2,3-hydroxylating) Definition trans-Cinnamate + Oxygen + NADH + H+ <=> cis-3-(3-Carboxyethenyl)-3,5-cyclohexadiene-1,2-diol + NAD+ Equation Comment HcaA1 HcaA2 HcaC HcaD Reaction class Enzyme Pathway rn00360   Phenylalanine metabolism rn01120   Microbial metabolism in diverse environments rn01220   Degradation of aromatic compounds Module M00545   Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA Orthology…

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KEGG REACTION: R06783

Entry R06783                      Reaction                                Name trans-cinnamate,NADH:oxygen oxidoreductase (2,3-hydroxylating) Definition trans-Cinnamate + Oxygen + NADH + H+ <=> cis-3-(3-Carboxyethenyl)-3,5-cyclohexadiene-1,2-diol + NAD+ Equation Comment HcaA1 HcaA2 HcaC HcaD Reaction class Enzyme Pathway rn00360   Phenylalanine metabolism rn01120   Microbial metabolism in diverse environments rn01220   Degradation of aromatic compounds Module M00545   Trans-cinnamate degradation, trans-cinnamate => acetyl-CoA Orthology…

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Bioinformatics Scientist at Infectious Disease Institute

IDI seeks to hire a Bioinformatics Scientist (BS) for the centre. The BS will be a fulltime staff who is familiar with the application of computational and biotechnology capabilities to biomedical and public health problems like genetics, clinical and medical research, as well as other data intensive analyses. By coordinating…

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KEGG pathway modules

KEGG pathway modules 0 Hi everyone, I’m looking to create a table with in the first column genes (ENSEMBL ID or symbol) and in the second column all the pathway modules in which the gene is involved. For example this should be the result: | Gene 1 | module 1,…

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Index of /~psgendb/doc/local/biopython-1.64.old/Tests/output

Name Last modified Size Description Parent Directory   –   test_AlignIO 2014-05-29 05:23 31K   test_AlignIO_FastaIO 2014-05-29 05:23 60K   test_ClustalOmega_tool 2014-05-29 05:23 1.2K   test_Clustalw 2014-05-29 05:23 5.8K   test_Clustalw_tool 2014-05-29 05:23 1.3K   test_CodonTable 2014-05-29 05:23 21   test_CodonUsage 2014-05-29 05:23 784   test_DocSQL 2014-05-29 05:23 42  …

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Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection

1. Latgé, J. P. and Chamilos, G. Aspergillus fumigatus and Aspergillosis in 2019. Clin. Microbiol. Rev. doi.org/10.1128/CMR.00140-18 (2019). 2. Invasive Aspergillosis. LIFE www.life-worldwide.org/fungal-diseases/invasive-aspergillosis (2020). 3. Harrison, N. et al. Incidence and characteristics of invasive fungal diseases in allogeneic hematopoietic stem cell transplant recipients: a retrospective cohort study. BMC Infect. Dis….

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KEGG COMPOUND: C15365

KEGG COMPOUND: C15365     COMPOUND: C15365 Help Entry C15365                      Compound                                Name 4-Pregnene-16alpha,21-diol-3,20-dione;16alpha,21-Dihydroxypregn-4-ene-3,20-dione Formula C21H30O4 Exact mass 346.2144 Mol weight 346.4605 Structure Mol fileKCF fileDB search Other DBs KCF data Show ATOM        25            1   C1y C    26.6870  -20.7306            2   C1y C    25.5683  -20.0954            3   C1y C    27.7943  -20.0837            4   C1x C    26.6637  -22.0009            5   C1z C    24.4728  -20.7423            6   C1x C    25.5624  -18.8134            7   C1z C    27.7943  -18.8018            8   C1x C    30.0204  -20.0896            9   C1x C    25.5800  -22.6419            10  C2y C    24.4728  -22.0126            11  C1x C    23.3715  -20.1130            12  C1a C    24.4552  -19.2680            13  C1x C    26.6754  -18.1667            14  C1y C    28.9189  -18.1608            15  C1y C    30.0261  -18.8077            16  C2x C    23.3715  -22.6536            17  C1x C    22.2876  -20.7423            18  C5a C    28.9189  -16.9021            19  C5x C    22.2876  -22.0126            20  C1b C    30.0087  -16.2845            21  C1a…

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KEGG COMPOUND: C12206

KEGG COMPOUND: C12206     COMPOUND: C12206 Help Entry C12206                      Compound                                Name Formula C9H10O3 Exact mass 166.063 Mol weight 166.1739 Structure Mol fileKCF fileDB search Reaction Pathway map00940   Phenylpropanoid biosynthesis map01110   Biosynthesis of secondary metabolites Enzyme Brite Phytochemical compounds [BR:br08003] Phenylpropanoids  Monolignols   Caffeate derivatives    C12206  Caffeyl alcohol BRITE hierarchy Other DBs KCF data Show ATOM        12            1   C8y C    28.0700  -19.5300            2   C8x C    28.0700  -20.9300            3   C8x…

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KEGG REACTION: R01945

Entry R01945                      Reaction                                Name Caffeoyl-CoA:quinate O-(3,4-dihydroxycinnamoyl)transferase Definition Caffeoyl-CoA + Quinate <=> CoA + Chlorogenate Equation Reaction class Enzyme Pathway rn00940   Phenylpropanoid biosynthesis rn00945   Stilbenoid, diarylheptanoid and gingerol biosynthesis rn01110   Biosynthesis of secondary metabolites Orthology Read more here: Source link

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KEGG REACTION: R08916

Entry R08916                      Reaction                                Name 3beta-hydroxy-9beta-pimara-7,15-diene-19,6beta-olide:NAD+ oxidoreductase Definition 3beta-Hydroxy-9beta-pimara-7,15-diene-19,6beta-olide + NAD+ <=> Momilactone A + NADH + H+ Equation Comment NADP+ (less effective, see R08917) Reaction class Enzyme Pathway rn00904   Diterpenoid biosynthesis rn01110   Biosynthesis of secondary metabolites Orthology Other DBs Read more here: Source link

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Diagnostic markers of AIDS combined with TM infection

Introduction The prevalence of Human immunodeficiency virus/Acquired Immune Deficiency Syndrome (HIV/AIDS) is still a public health problem that threatens the health of all human beings. According to the latest report of the World Health Organization, in the end of 2019, there were 38 million patients with human immunodeficiency virus/acquired immunodeficiency…

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KEGG ENZYME: 1.14.11.57

Entry EC 1.14.11.57               Enzyme                                  Name L-proline trans-4-hydroxylase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donorBRITE hierarchy Sysname L-proline,2-oxoglutarate:oxygen oxidoreductase (trans-4-hydroxylating) Reaction(IUBMB) L-proline + 2-oxoglutarate + O2 = trans-4-hydroxy-L-proline + succinate + CO2 [RN:R01252] Reaction(KEGG)…

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Finding differential subpathways of metabolic networks using RNA-seq data

Finding differential subpathways of metabolic networks using RNA-seq data 0 I would like to find a good approach or R/Python package that would help me to find differential subpathways of selected KEGG metabolic pathways. As input, I have expression data of N samples or differential expression data for G group…

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Gene Id Conversion Tool

MyGene.info is a web service that provides up to date annotations in several fields and is great for gene ID conversion. All species from NCBI and Ensembl are supported and annotations are updated weekly to ensure the latest annotations are available. Both python and R/Bioconductor clients are easy to use….

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Bioinformatics analysis pinpoints the pathways involved in intestinal SARS/CoV-2 infection

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is a positive-strand RNA virus, which appears spherical under a transmission electron microscope. Many studies have shown that SARS-CoV-2 infects host cells via the interaction between the viral spike protein and the host receptor, angiotensin-converting enzyme II (ACE2). SARS-CoV-2 can spread through…

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WGCNA Analysis Identifies Polycystic Ovary Syndrome-Associated Circula

Introduction Polycystic ovary syndrome (PCOS) is a common endocrine metabolic disorder in women of childbearing age.1 PCOS patients are typically characterized by androgen excess, polycystic ovaries and anovulation, and are often accompanied by insulin resistance and obesity.2 Consequently, patients with this syndrome not only suffer from infertility,3 but also have…

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kegg pathway

kegg pathway 1 what is the significance of KEGG pathway in biological annotation of genes. kegg pathway • 23 views • link updated 1 minute ago by seidel 8.5k • written 2 hours ago by Julia • 0 KEGG is a way of mapping how genes work together and contribute…

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a question about using Enrichr

a question about using Enrichr 0 Hi, I have a question about using Enrich r. Actually I am using Enrichr for analyzing a set of microarray data to find out the most enriched pathways considering a list of down regulated genes. However, I am not sure how to annotate the…

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KEGG COMPOUND: C14321

KEGG COMPOUND: C14321     COMPOUND: C14321 Help Entry C14321                      Compound                                Name Benzo[k]fluoranthene;11,12-Benzofluoranthene Formula C20H12 Exact mass 252.0939 Mol weight 252.3093 Structure Mol fileKCF fileDB search Other DBs KCF data Show ATOM        20            1   C8x C    23.5937  -16.9983            2   C8x C    23.5937  -18.3568            3   C8x C    24.7702  -19.0361            4   C8y C    25.9468  -18.3568            5   C8y C    25.9468  -16.9983            6   C8x C    24.7702  -16.3190            7   C8x C    27.1233  -19.0361            8   C8y C    28.2998  -18.3568            9   C8y C    28.2998  -16.9983            10  C8x C    27.1233  -16.3190            11  C8y C    30.6529  -18.3568            12  C8y C    30.6529  -16.9983            13  C8y C    29.4764  -16.3190            14  C8y C    31.8294  -16.3190            15  C8x C    31.8294  -14.9604            16  C8x C    30.6529  -14.2811            17  C8x C    29.4764  -14.9604            18  C8x C    31.8294  -19.0361            19  C8x C    33.0061  -18.3568            20  C8x C    33.0061  -16.9983BOND        24            1     1   2…

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KEGG COMPOUND: C14321

KEGG COMPOUND: C14321     COMPOUND: C14321 Help Entry C14321                      Compound                                Name Benzo[k]fluoranthene;11,12-Benzofluoranthene Formula C20H12 Exact mass 252.0939 Mol weight 252.3093 Structure Mol fileKCF fileDB search Other DBs KCF data Show ATOM        20            1   C8x C    23.5937  -16.9983            2   C8x C    23.5937  -18.3568            3   C8x C    24.7702  -19.0361            4   C8y C    25.9468  -18.3568            5   C8y C    25.9468  -16.9983            6   C8x C    24.7702  -16.3190            7   C8x C    27.1233  -19.0361            8   C8y C    28.2998  -18.3568            9   C8y C    28.2998  -16.9983            10  C8x C    27.1233  -16.3190            11  C8y C    30.6529  -18.3568            12  C8y C    30.6529  -16.9983            13  C8y C    29.4764  -16.3190            14  C8y C    31.8294  -16.3190            15  C8x C    31.8294  -14.9604            16  C8x C    30.6529  -14.2811            17  C8x C    29.4764  -14.9604            18  C8x C    31.8294  -19.0361            19  C8x C    33.0061  -18.3568            20  C8x C    33.0061  -16.9983BOND        24            1     1   2…

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Index of /~psgendb/local/biopython-1.64.old/Bio

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

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KEGG COMPOUND: C05629

KEGG COMPOUND: C05629     COMPOUND: C05629 Help Entry C05629                      Compound                                Name Phenylpropanoate;3-Phenylpropanoate;3-Phenyl-propionic acid;3-Phenylpropanoic acid;3-Phenylpropionic acid Formula C9H10O2 Exact mass 150.0681 Mol weight 150.1745 Structure Mol fileKCF fileDB search Reaction Pathway map01120   Microbial metabolism in diverse environments map01220   Degradation of aromatic compounds Enzyme Other DBs KCF data Show ATOM        11            1   C8y C    28.1642  -20.9195            2   C1b C    28.1577  -19.5290            3   C8x C    26.9594  -21.6180            4   C8x…

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KEGG REACTION: R01398

Entry RC00096                     RClass                                  Definition Reactant pair Related class DB search Reaction Enzyme Pathway rn00120   Primary bile acid biosynthesis rn00260   Glycine, serine and threonine metabolism rn00330   Arginine and proline metabolism rn00430   Taurine and hypotaurine metabolism rn00440   Phosphonate and phosphinate metabolism rn00460   Cyanoamino acid metabolism rn00524   Neomycin, kanamycin and gentamicin biosynthesis rn00550   Peptidoglycan…

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KEGG REACTION: R01398

Entry RC00096                     RClass                                  Definition Reactant pair Related class DB search Reaction Enzyme Pathway rn00120   Primary bile acid biosynthesis rn00260   Glycine, serine and threonine metabolism rn00330   Arginine and proline metabolism rn00430   Taurine and hypotaurine metabolism rn00440   Phosphonate and phosphinate metabolism rn00460   Cyanoamino acid metabolism rn00524   Neomycin, kanamycin and gentamicin biosynthesis rn00550   Peptidoglycan…

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KEGG REACTION: R04125

Entry R04125                      Reaction                                Name [protein]-S8-aminomethyldihydrolipoyllysine:tetrahydrofolate aminomethyltransferase (ammonia-forming) Definition [Protein]-S8-aminomethyldihydrolipoyllysine + Tetrahydrofolate <=> Dihydrolipoylprotein + 5,10-Methylenetetrahydrofolate + Ammonia Equation Comment Reaction class Enzyme Pathway rn00260   Glycine, serine and threonine metabolism rn00670   One carbon pool by folate Orthology Other DBs Read more here: Source link

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KEGG COMPOUND: C19566

KEGG COMPOUND: C19566     COMPOUND: C19566 Help Entry C19566                      Compound                                Name 4-Hydroxy-4-(methylnitrosoamino)-1-(3-pyridinyl)-1-butanone Formula C10H13N3O3 Exact mass 223.0957 Mol weight 223.2285 Structure Mol fileKCF fileDB search Reaction Pathway map00980   Metabolism of xenobiotics by cytochrome P450 map05204   Chemical carcinogenesis – DNA adducts Enzyme Other DBs KCF data Show ATOM        16            1   N5x N    18.0419  -19.7673            2   C8x C    18.0419  -21.1643            3   C8x C    19.2517  -21.8628            4   C8x C    20.4616  -21.1643            5   C8y…

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KEGG ENZYME: 2.3.1.98

KEGG ENZYME: 2.3.1.98     ENZYME: 2.3.1.98 Help Entry EC 2.3.1.98                 Enzyme                                  Name chlorogenate—glucarate O-hydroxycinnamoyltransferase;chlorogenate:glucarate caffeoyltransferase;chlorogenic acid:glucaric acid O-caffeoyltransferase;chlorogenate:glucarate caffeoyltransferase Class Transferases;Acyltransferases;Transferring groups other than aminoacyl groupsBRITE hierarchy Sysname chlorogenate:glucarate O-(hydroxycinnamoyl)transferase Reaction(IUBMB) chlorogenate + glucarate = quinate + 2-O-caffeoylglucarate [RN:R02998] Reaction(KEGG) Substrate Product Comment Galactarate can act as acceptor, more slowly. Involved with…

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KEGG T01001: 2850

Entry 2850              CDS       T01001                                  Symbol GPR27, SREB1 Name (RefSeq) G protein-coupled receptor 27   KO K04301   super conserved receptor expressed in brain 1 Organism hsa  Homo sapiens (human) Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   04030 G protein-coupled receptors [BR:hsa04030]    2850 (GPR27)G protein-coupled receptors [BR:hsa04030] Rhodopsin family  Others   Super conserved receptor expressed in…

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KEGG ENZYME: 1.1.99.18

Entry EC 1.1.99.18                Enzyme                                  Name cellobiose dehydrogenase (acceptor);cellobiose dehydrogenase;cellobiose oxidoreductase;Phanerochaete chrysosporium cellobiose oxidoreductase;CBOR;cellobiose oxidase;cellobiose:oxygen 1-oxidoreductase;CDH;cellobiose:(acceptor) 1-oxidoreductase Class Oxidoreductases;Acting on the CH-OH group of donors;With unknown physiological acceptorsBRITE hierarchy Sysname cellobiose:acceptor 1-oxidoreductase Reaction(IUBMB) cellobiose + acceptor = cellobiono-1,5-lactone + reduced acceptor [RN:R01443 R06246] Reaction(KEGG) Substrate Product cellobiono-1,5-lactone [CPD:C01093]; reduced acceptor [CPD:C00030] Comment Also…

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KEGG T01001: 9997

KEGG T01001: 9997     Homo sapiens (human): 9997 Help Entry 9997              CDS       T01001                                  Symbol SCO2, CEMCOX1, ECGF1, Gliostatin, MC4DN2, MYP6, PD-ECGF, SCO1L, TP, TYMP, TdRPase Name (RefSeq) synthesis of cytochrome C oxidase 2   KO Organism hsa  Homo sapiens (human) Pathway hsa05230   Central carbon metabolism in cancer Disease H01200   Fatal infantile cardioencephalomyopathy H01368   Cytochrome…

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KEGG REACTION: R09152

Entry R09152                      Reaction                                Name trichloroethene,NADH:oxygen oxidoreductase (formate-forming) Definition Trichloroethene + Oxygen + 2 H2O + NADH + H+ <=> 2 Formate + 3 Hydrochloric acid + NAD+ Equation Comment Reaction class Enzyme Pathway rn00625   Chloroalkane and chloroalkene degradation rn01120   Microbial metabolism in diverse environments Orthology K18089   benzene/toluene/chlorobenzene dioxygenase ferredoxin component K18090  …

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circRNA-miRNA-mRNA regulatory network in atrial fibrillation

Introduction Atrial fibrillation (AF) is the most common type of arrhythmia in clinical practice, with global prevalence continuing to increase primarily with age.1 In China, 6.5 persons out of every thousand suffer from AF, and there are about 3.9 million patients with AF who are over 60 years old, but…

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KEGG COMPOUND: C21461

KEGG COMPOUND: C21461     COMPOUND: C21461 Help Entry C21461                      Compound                                Name Kdo2-lipid A 1-(2-aminoethyl diphosphate) Formula C112H208N3O42P3 Exact mass 2360.3445 Mol weight 2361.7661 Structure Mol fileKCF fileDB search Reaction Pathway map00540   Lipopolysaccharide biosynthesis Enzyme Other DBs KCF data Show ATOM        160            1   C1y C    15.2440  -13.5657            2   C1y C    16.4327  -12.8664            3   C1y C    14.0552  -12.8664            4   O7a O    15.2440  -14.9642            5   C1y C    16.4327  -11.4679            6   N1b N    17.6215  -13.5657            7   C1y C    14.0552  -11.4679            8   O2b O    12.7966  -13.5657            9   C7a C    14.0552  -15.6635            10  O2x O    15.2440  -10.7686            11  O2a O    17.6215  -10.7686            12  C5a…

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KEGG COMPOUND: C00144

KEGG COMPOUND: C00144     COMPOUND: C00144 Help Entry C00144                      Compound                                Name GMP;Guanosine 5′-phosphate;Guanosine monophosphate;Guanosine 5′-monophosphate;Guanylic acid Formula C10H14N5O8P Exact mass 363.058 Mol weight 363.2206 Structure Mol fileKCF fileDB search Reaction Pathway map01060   Biosynthesis of plant secondary metabolites map01065   Biosynthesis of alkaloids derived from histidine and purine Module M00050   Guanine ribonucleotide biosynthesis,…

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KEGG ENZYME: 2.6.1.15

Entry EC 2.6.1.15                 Enzyme                                  Name glutamine—pyruvate transaminase;glutaminase II;L-glutamine transaminase L;glutamine-oxo-acid transaminase Class Transferases;Transferring nitrogenous groups;TransaminasesBRITE hierarchy Sysname L-glutamine:pyruvate aminotransferase Reaction(IUBMB) L-glutamine + pyruvate = 2-oxoglutaramate + L-alanine [RN:R00576] Reaction(KEGG) Substrate Product Comment A pyridoxal-phosphate protein. L-Methionine can act as donor; glyoxylate can act as acceptor. History EC 2.6.1.15 created 1961 Pathway ec00250  …

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KEGG ENZYME: 2.6.1.57

Entry EC 2.6.1.57                 Enzyme                                  Name aromatic-amino-acid transaminase;aromatic amino acid aminotransferase;aromatic aminotransferase;ArAT Class Transferases;Transferring nitrogenous groups;TransaminasesBRITE hierarchy Sysname aromatic-amino-acid:2-oxoglutarate aminotransferase Reaction(IUBMB) an aromatic amino acid + 2-oxoglutarate = an aromatic oxo acid + L-glutamate [RN:R03120] Reaction(KEGG) R03120 > R00694 R00734 R10845; (other) R01731 R07396 Reaction Substrate aromatic amino acid [CPD:C01021]; 2-oxoglutarate [CPD:C00026] Product…

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Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Introduction Corn and soybean meal are the main components of high energy and high protein diets for pigs and are also the main raw materials of food products for human consumption, fermentation, and bioenergy industry (Sevillano et al., 2018). As the arable land of food crops was limited whereas the…

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Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Introduction Corn and soybean meal are the main components of high energy and high protein diets for pigs and are also the main raw materials of food products for human consumption, fermentation, and bioenergy industry (Sevillano et al., 2018). As the arable land of food crops was limited whereas the…

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KEGG ENZYME: 1.14.14.83

Entry EC 1.14.14.83               Enzyme                                  Name geraniol 8-hydroxylase;CYP76B6 (gene name);G10H (gene name) Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donorBRITE hierarchy Sysname geraniol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (8-hydroxylating) Reaction(IUBMB) geraniol + [reduced…

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KEGG ORTHOLOGY: K19378

Entry K19378                      KO                                      Symbol H Name Morbillivirus hemagglutinin glycoprotein Pathway Network   Element N00684   MV F/H to CD28-PI3K signaling pathway Brite KEGG Orthology (KO) [BR:ko00001] 09120 Genetic Information Processing  09125 Information processing in viruses   03230 Viral genome structure    K19378  H; Morbillivirus hemagglutinin glycoprotein 09160 Human Diseases  09172 Infectious disease: viral   05162 Measles    K19378  H; Morbillivirus hemagglutinin glycoprotein 09180 Brite Hierarchies  09185 Viral protein families   03200…

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Transcriptome Sequencing Explores the Mechanism of Baicalin on Bone Ca

Introduction With the continuous improvement of cancer treatment technology, the 3-year and 5-year survival rates of cancer patients have been greatly improved. However, cancer still cause pain to the patients, which seriously affects their quality of life. This is because in many common cancers, tumors can easily metastase to the…

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KEGG ORTHOLOGY: K22004

Entry EC 4.1.1.113                Enzyme                                  Name trans-aconitate decarboxylase;TAD1 (gene name) Class Lyases;Carbon-carbon lyases;Carboxy-lyasesBRITE hierarchy Sysname trans-aconitate carboxy-lyase (itaconate-forming) Reaction(IUBMB) trans-aconitate = itaconate + CO2 [RN:R11749] Reaction(KEGG) R11749 Reaction Substrate trans-aconitate [CPD:C02341] Product itaconate [CPD:C00490]; CO2 [CPD:C00011] Comment The enzyme, characterized from the smut fungus Ustilago maydis, is involved in an alternative pathway for…

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Genes and Pathways Involved in Postmenopausal Osteoporosis

Introduction Many postmenopausal women suffer from postmenopausal osteoporosis (PMO). A survey of 3247 Italian postmenopausal women found that according to bone mineral density (BMD) diagnostic criteria, the prevalence of osteoporosis was 36.6%.1 PMO patients may suffer from chronic pain and fractures, and as a result their quality of life is…

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KEGG COMPOUND: C01585

KEGG COMPOUND: C01585     COMPOUND: C01585 Help Entry C01585                      Compound                                Name Hexanoic acid;Hexanoate;Hexylic acid;n-Caproic acid Formula C6H12O2 Exact mass 116.0837 Mol weight 116.1583 Structure Mol fileKCF fileDB search Reaction Enzyme Brite Compounds with biological roles [BR:br08001] Organic acids  Carboxylic acids   Monocarboxylic acids    C01585  Capronate; Hexanoate Lipids  Fatty acids   Saturated fatty acids    C01585  Caproic acid (6:0)Lipids [BR:br08002] FA  Fatty acyls  FA01 Fatty Acids and Conjugates   FA0101…

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KEGG COMPOUND: C01585

KEGG COMPOUND: C01585     COMPOUND: C01585 Help Entry C01585                      Compound                                Name Hexanoic acid;Hexanoate;Hexylic acid;n-Caproic acid Formula C6H12O2 Exact mass 116.0837 Mol weight 116.1583 Structure Mol fileKCF fileDB search Reaction Enzyme Brite Compounds with biological roles [BR:br08001] Organic acids  Carboxylic acids   Monocarboxylic acids    C01585  Capronate; Hexanoate Lipids  Fatty acids   Saturated fatty acids    C01585  Caproic acid (6:0)Lipids [BR:br08002] FA  Fatty acyls  FA01 Fatty Acids and Conjugates   FA0101…

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KEGG COMPOUND: C06032

KEGG COMPOUND: C06032     COMPOUND: C06032 Help Entry C06032                      Compound                                Name D-erythro-3-Methylmalate;(2R,3S)-3-Methylmalate Formula C5H8O5 Exact mass 148.0372 Mol weight 148.114 Structure Mol fileKCF fileDB search Reaction Pathway map00290   Valine, leucine and isoleucine biosynthesis map00660   C5-Branched dibasic acid metabolism map01210   2-Oxocarboxylic acid metabolism Module M00535   Isoleucine biosynthesis, pyruvate => 2-oxobutanoate Enzyme Other…

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[Analysis on the expression profile of circRNAs in hypertrophic myocardium mice]

Objective: To explore the differential expression of circRNAs and their potential impact on the pathophysiological process in cardiac hypertrophy. Methods: Six SPF C57BL/6J male mice, aged 8 to 10 weeks, were randomly divided into transverse aortic constriction (TAC) group (n=3) or sham operation(sham) group (n=3) according to random number table…

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KEGG ENZYME: 4.1.1.5

Entry EC 4.1.1.5                  Enzyme                                  Name acetolactate decarboxylase;alpha-acetolactate decarboxylase;(S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase;(S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase [(R)-2-acetoin-forming];(S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase [(3R)-3-hydroxybutan-2-one-forming] Class Lyases;Carbon-carbon lyases;Carboxy-lyasesBRITE hierarchy Sysname (2S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase [(3R)-3-hydroxybutan-2-one-forming] Reaction(IUBMB) (2S)-2-hydroxy-2-methyl-3-oxobutanoate = (3R)-3-hydroxybutan-2-one + CO2 [RN:R02948] Reaction(KEGG) Substrate (2S)-2-hydroxy-2-methyl-3-oxobutanoate [CPD:C06010] Product (3R)-3-hydroxybutan-2-one; CO2 [CPD:C00011] History EC 4.1.1.5 created 1961 Pathway ec00660   C5-Branched dibasic acid metabolism ec01110   Biosynthesis of secondary metabolites…

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Finding players and targets of expression-regulating pathways

I am currently working on a project involving using pathways to group genes. However, I am quite new to the field, so I have a some (beginner) questions concerning the biology and available databases. A) I have heard about the concept of dividing the genes interacting in pathways into players,…

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Frontiers | Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses

Introduction Phytoplasmas are wall-less bacterial pathogens that are known to infect numerous plant species and lead to significant agricultural losses (Gurr et al., 2016; Kumari et al., 2019; Pierro et al., 2019). They are parasitic bacteria multiplying exclusively in phloem sieve elements and are transmitted between plants by phloem-feeding insects…

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T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling

This article was originally published here Bioinformatics. 2021 Nov 10:btab770. doi: 10.1093/bioinformatics/btab770. Online ahead of print. ABSTRACT MOTIVATION: A major task in genetic studies is to identify genes related to human diseases and traits to understand functional characteristics of genetic mutations and enhance patient diagnosis. Compared to marginal analyses of…

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Bioconductor – MetaboSignal (development version)

DOI: 10.18129/B9.bioc.MetaboSignal     This is the development version of MetaboSignal; for the stable release version, see MetaboSignal. MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways Bioconductor version: Development (3.15) MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG…

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Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service | BMC Bioinformatics

Since the opening of the open-ended Call in February 2020 [30], Laniakea@ReCaS has accepted ten project proposals for a total of 18 Galaxy instances operating on the ReCaS infrastructure that altogether launched almost 30 k jobs, as of March 2021 (Fig. 3). Fig. 3 Cumulative number of jobs launched by all the…

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ARGs as potential biomarkers & therapeutic targets in AF

Introduction Atrial fibrillation (AF) is the most common clinically sustained cardiac rhythm disorder. There is a high prevalence of AF all over the world, the highest in North America, Europe, China, and Southeast Asia, with approximately 270–360 cases per 100,000 people.1 Due to the lack of understanding of the pathogenesis…

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KEGG ENZYME: 4.3.2.9

Entry EC 4.3.2.9                  Enzyme                                  Name gamma-glutamylcyclotransferase;gamma-glutamyl-amino acid cyclotransferase;gamma-L-glutamylcyclotransferase;L-glutamic cyclase;(5-L-glutamyl)-L-amino-acid 5-glutamyltransferase (cyclizing);GGCT Class Lyases;Carbon-nitrogen lyases;Amidine-lyasesBRITE hierarchy Sysname alpha-(gamma-L-glutamyl)-L-amino-acid gamma-glutamyl cyclotransferase (5-oxo-L-proline producing) Reaction(IUBMB) alpha-(gamma-L-glutamyl)-L-amino acid = alpha-L-amino acid + 5-oxo-L-proline [RN:R03749] Reaction(KEGG) Substrate alpha-(gamma-L-glutamyl)-L-amino acid [CPD:C03740] Product alpha-L-amino acid; 5-oxo-L-proline [CPD:C01879] Comment The enzyme, found in animals and plants, acts on derivatives of…

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Candidate genes associated with synovial macrophages

Jia Xu,1 Ming-Ying Zhang,2 Wei Jiao,1 Cong-Qi Hu,1 Dan-Bin Wu,2 Jia-Hui Yu,1 Guang-Xing Chen2,3 1First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China; 2Department of Rheumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China;…

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Exploration of Prognostic Biomarkers of Muscle-Invasive Bladder Cancer (MIBC) by Bioinformatics

This article was originally published here Evol Bioinform Online. 2021 Oct 28;17:11769343211049270. doi: 10.1177/11769343211049270. eCollection 2021. ABSTRACT We aimed to discover prognostic factors of muscle-invasive bladder cancer (MIBC) and investigate their relationship with immune therapies. Online data of MIBC were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression…

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Bioinformatics analysis to screen DNA methylation-driven genes for prognosis of patients with bladder cancer

This article was originally published here Transl Androl Urol. 2021 Sep;10(9):3604-3619. doi: 10.21037/tau-21-326. ABSTRACT BACKGROUND: Bladder cancer (BLCA) is the most prevalent tumor affecting the urinary system, and has contributed to a rise in morbidity and mortality rates. Herein, we sought to identify the methylation-driven genes (MDGs)of BLCA in an…

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KEGG Pathway and ID convertion problem

KEGG Pathway and ID convertion problem 0 Hello there! I am currently having a problem with ID convertion between different databases. What I did; I made meta-analyses of Beta vulgaris and found 10 genes with their ENSEMBL ID’s. So in order to create KEGG pathways through r package “pathview”, converted…

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Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator

1. Pérez, J., Moraleda-Muñoz, A., Marcos-Torres, F. J. & Muñoz-Dorado, J. Bacterial predation: 75 years and counting!. Environ. Microbiol. 18, 766–779 (2016). PubMed  Article  PubMed Central  Google Scholar  2. Linares-Otoya, L. et al. Diversity and antimicrobial potential of predatory bacteria from the Peruvian coastline. Mar. Drugs. 15, E308. doi.org/10.3390/md15100308 (2017)….

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KEGG ENZYME: 4.99.1.10

Entry EC 4.99.1.10                Enzyme                                  Name magnesium dechelatase;SGR (gene name);SGRL (gene name);Mg-dechelatase Class Lyases;Other lyases;Sole sub-subclass for lyases that do not belong in the other subclassesBRITE hierarchy Sysname chlorophyll a magnesium lyase Reaction(IUBMB) (1) chlorophyll a + 2 H+ = pheophytin a + Mg2+ [RN:R08584]; (2) chlorophyllide a + 2 H+ = pheophorbide…

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What kind of libraries in Enrichr should I use?

What kind of libraries in Enrichr should I use? 0 I performed bulk RNA-seq using animal brain tissues with and without injury. Among DEGs from RNA-seq (injury vs control), I’d like to choose candidate genes involved with cellular changes after brain injury using Enrichr. As you know, however, there are…

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KEGG ENZYME: 2.4.1.366

Entry EC 2.4.1.366                Enzyme                                  Name ginsenoside F1 6-O-glucosyltransferase;UGTPg101 (gene name) Class Transferases;Glycosyltransferases;HexosyltransferasesBRITE hierarchy Sysname UDP-alpha-D-glucose:ginsenoside F1 6-O-glucosyltransferase Reaction(IUBMB) UDP-alpha-D-glucose + ginsenoside F1 = UDP + (20S)-ginsenoside Rg1 [RN:R12387] Reaction(KEGG) Substrate UDP-alpha-D-glucose [CPD:C00029]; ginsenoside F1 [CPD:C20780] Product Comment The enzyme, characterized from the plant Panax ginseng, glucosylates the C-6 position of ginsenoside F1….

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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Editing KEGG Pathways in R

Editing KEGG Pathways in R 0 Hello, I’m relatively new to programming and bioinformatics and so far, have learned most of the fundamentals of R, several Bioconductor packages, gene enrichment analysis as well as some of the common pathway databases to map my data over (i.e., KEGG, REACTOME, wikipathways etc)….

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KEGG GENOME: Homo sapiens (human)

Entry T01001            Complete  Genome                                  Org code hsa Name Category Reference genome Annotation yesShow organism Taxonomy   Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Taxonomy Data source Original DB Statistics Number of protein genes:       19557Number of RNA genes:            2642 Created 2000 Reference   Authors Lander ES, Linton LM, Birren B, Nusbaum…

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KEGG COMPOUND: C00222

Entry C00222                      Compound                                Name 3-Oxopropanoate;Malonate semialdehyde Formula C3H4O3 Exact mass 88.016 Mol weight 88.0621 Structure Mol fileKCF fileDB search Reaction Pathway map00562   Inositol phosphate metabolism map00625   Chloroalkane and chloroalkene degradation map00720   Carbon fixation pathways in prokaryotes map01120   Microbial metabolism in diverse environments Module M00013   Malonate semialdehyde pathway, propanoyl-CoA => acetyl-CoA M00375  …

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Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species

Tool:SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species 1 Dear all, The new SBGNview package has been released with major updates and improvement: GitHub github.com/datapplab/SBGNview BioC bioconductor.org/packages/SBGNview/ SBGNview is a tool set for pathway based data visualization, integration and analysis. SBGNview is similar and complementary to the widely…

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copper c23400 in rok

KEGG ENZYME: 1.15.1.1 EC 1.15.1.1 Enzyme. A metalloprotein also known as erythrocuprein, hemocuprein or cytocuprein. Enzymes from most eukaryotes contain both copper and zinc those from…

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KEGG ENZYME: 2.4.99.1

Entry EC 2.4.99.1                 Enzyme                                  Name beta-galactoside alpha-(2,6)-sialyltransferase;ST6Gal-I;CMP-N-acetylneuraminate:beta-D-galactosyl-1,4-N-acetyl-beta-D-glucosamine alpha-2,6-N-acetylneuraminyltransferase;lactosylceramide alpha-2,6-N-sialyltransferase;CMP-N-acetylneuraminate:beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosamine alpha-(2->6)-N-acetylneuraminyltransferase;beta-galactoside alpha-2,6-sialyltransferase Class Transferases;Glycosyltransferases;Transferring other glycosyl groupsBRITE hierarchy Sysname CMP-N-acetyl-beta-neuraminate:beta-D-galactoside alpha-(2->6)-N-acetylneuraminyltransferase (configuration-inverting) Reaction(IUBMB) CMP-N-acetyl-beta-neuraminate + beta-D-galactosyl-R = CMP + N-acetyl-alpha-neuraminyl-(2->6)-beta-D-galactosyl-R [RN:R04532 R06188] Reaction(KEGG) Substrate CMP-N-acetyl-beta-neuraminate [CPD:C00128]; beta-D-galactosyl-R [CPD:C02900] Product CMP [CPD:C00055]; N-acetyl-alpha-neuraminyl-(2->6)-beta-D-galactosyl-R Comment The enzyme acts on the terminal non-reducing beta-D-galactosyl residue of…

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KEGG ENZYME: 2.5.1.101

Entry EC 2.5.1.101                Enzyme                                  Name N,N’-diacetyllegionaminate synthase;neuB (gene name);legI (gene name) Class Transferases;Transferring alkyl or aryl groups, other than methyl groups;Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)BRITE hierarchy Sysname phosphoenolpyruvate:2,4-diacetamido-2,4,6-trideoxy-alpha-D-mannopyranose 1-(2-carboxy-2-oxoethyl)transferase Reaction(IUBMB) 2,4-diacetamido-2,4,6-trideoxy-alpha-D-mannopyranose + phosphoenolpyruvate + H2O = N,N’-diacetyllegionaminate + phosphate [RN:R10304] Reaction(KEGG) Substrate 2,4-diacetamido-2,4,6-trideoxy-alpha-D-mannopyranose…

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KEGG ENZYME: 1.1.1.299

Entry EC 1.1.1.299                Enzyme                                  Name malate dehydrogenase [NAD(P)+];MdH II, NAD(P)+-dependent malate dehyrogenase Class Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname (S)-malate:NAD(P)+ oxidoreductase Reaction(IUBMB) (S)-malate + NAD(P)+ = oxaloacetate + NAD(P)H + H+ [RN:R00342 R00343] Reaction(KEGG) Substrate Product Comment This enzyme, which was characterized from the…

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KEGG ENZYME: 1.1.99.6

Entry EC 1.1.99.6                 Enzyme                                  Name D-lactate dehydrogenase (acceptor);D-2-hydroxy acid dehydrogenase;D-2-hydroxy-acid dehydrogenase;(R)-2-hydroxy-acid:acceptor 2-oxidoreductase Class Oxidoreductases;Acting on the CH-OH group of donors;With unknown physiological acceptorsBRITE hierarchy Sysname (R)-lactate:acceptor 2-oxidoreductase Reaction(IUBMB) (R)-lactate + acceptor = pyruvate + reduced acceptor [RN:R00297] Reaction(KEGG) R00297 Reaction Substrate (R)-lactate [CPD:C00256]; acceptor [CPD:C00028] Product pyruvate [CPD:C00022]; reduced acceptor [CPD:C00030] Comment…

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KEGG ENZYME: 1.2.1.51

Entry EC 1.2.1.51                 Enzyme                                  Name pyruvate dehydrogenase (NADP+) Class Oxidoreductases;Acting on the aldehyde or oxo group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname pyruvate:NADP+ 2-oxidoreductase (CoA-acetylating) Reaction(IUBMB) pyruvate + CoA + NADP+ = acetyl-CoA + CO2 + NADPH [RN:R00210] Reaction(KEGG) Substrate Product Comment The Euglena enzyme can also use FAD…

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A list of human cell cycle genes for Seurat

A list of human cell cycle genes for Seurat 1 Hi! First of all I apologize if this question has already been asked. I googled the hell out it but couldn’t find any help. So my exact question is: where can I get a list of human cell cycle genes…

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Identification of Significant Genes in Lung Cancer of Nonsmoking Women via Bioinformatics Analysis

This article was originally published here Biomed Res Int. 2021 Oct 11;2021:5516218. doi: 10.1155/2021/5516218. eCollection 2021. ABSTRACT BACKGROUND: The aim of this study was to identify potential key genes, proteins, and associated interaction networks for the development of lung cancer in nonsmoking women through a bioinformatics approach. METHODS: We used…

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LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

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Need old kegg database v67.1

Need old kegg database v67.1 0 I am in need of Annotation rest data (like that of rest.kegg.jp/link/Ko/reaction) but of a quite an old version. The version of the database that I’m looking for is (67.1). I need KO to R, RPAIRs,RP data from KEGG DB v. 67.1 . I…

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KEGG passway analysis after Seurat analysis

KEGG passway analysis after Seurat analysis 0 Hello, everyone. I am so sorry for this amateur question. I have a scRNA-seq data and want to compare and visualize the expression levels across genes on a cluster by using clusterprofiler package (passway analysis), but I think the average expression levels of…

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KEGG ENZYME: 2.5.1.34

Entry EC 2.5.1.34                 Enzyme                                  Name 4-dimethylallyltryptophan synthase;dimethylallylpyrophosphate:L-tryptophan dimethylallyltransferase;dimethylallyltryptophan synthetase;dimethylallylpyrophosphate:tryptophan dimethylallyl transferase;DMAT synthetase;4-(gamma,gamma-dimethylallyl)tryptophan synthase;tryptophan dimethylallyltransferase Class Transferases;Transferring alkyl or aryl groups, other than methyl groups;Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)BRITE hierarchy Sysname dimethylallyl-diphosphate:L-tryptophan 4-dimethylallyltransferase Reaction(IUBMB) dimethylallyl diphosphate + L-tryptophan = diphosphate + 4-(3-methylbut-2-enyl)-L-tryptophan [RN:R01657] Reaction(KEGG)…

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KEGG ENZYME: 2.4.1.372

Entry EC 2.4.1.372                Enzyme                                  Name mutansucrase;gtfJ (gene name) Class Transferases;Glycosyltransferases;HexosyltransferasesBRITE hierarchy Sysname sucrose:(1->3)-alpha-D-glucan 3-alpha-D-glucosyltransferase Reaction(IUBMB) sucrose + [(1->3)-alpha-D-glucosyl]n = D-fructose + [(1->3)-alpha-D-glucosyl]n+1 [RN:R12527] Reaction(KEGG) Substrate sucrose [CPD:C00089]; [(1->3)-alpha-D-glucosyl]n [CPD:C02616] Product D-fructose [CPD:C00095]; [(1->3)-alpha-D-glucosyl]n+1 Comment The glucansucrases transfer a D-glucosyl residue from sucrose to a glucan chain. They are classified based on the…

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Synchronous rectal tumours in a patient with Lynch syndrome

Plain Language Summary The increasingly widespread use of immunohistochemistry and next-generation sequencing in the detection of microsatellite instability (MSI) and DNA mismatch repair (MMR) status has led to the observation of various unusual tumour types that exhibit MMR protein deficiency in Lynch syndrome. Here, we report a case of two…

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How do I output the results of KEGG analysis?

How do I output the results of KEGG analysis? 0 Hi, all. I have performed KEGG analysis in KEGG home page as following. But I don’t know how to output the results. Is there any way to output it in KEGG HP? Or should I use R package? I would…

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How to do gene enrichment with locally stored KEGG & Reactome data in R

How to do gene enrichment with locally stored KEGG & Reactome data in R 0 Hi all, For a collaboration project we are required to use R-studio in a remote environment. They have also provided the data from KEGG and Reactome on the same server, which we can access. I’m…

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H/ACA snoRNP gene family as diagnostic/prognostic biomarkers

Introduction Primary liver cancer, including hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma, is the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related deaths worldwide.1 High metastasis and recurrence rates, as well as limited treatment options, lead to the poor prognosis of advanced HCC.2 Among patients diagnosed with…

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A TME-Related Signature as a Biomarker in Liver Cancer

Introduction As one of the most frequent causes of cancer deaths across the globe, liver cancer, characterized by high mortality, recurrence, metastasis and poor prognosis, is the only one of the top five deadliest cancers to have an annual percentage increase in occurrence.1 Surgery, local destructive therapies, and liver transplantation…

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KEGG ENZYME: 1.1.1.124

KEGG ENZYME: 1.1.1.124     ENZYME: 1.1.1.124 Help Entry EC 1.1.1.124                Enzyme                                  Name fructose 5-dehydrogenase (NADP+);5-ketofructose reductase (NADP+);5-keto-D-fructose reductase (NADP+);fructose 5-(nicotinamide adenine dinucleotide phosphate) dehydrogenase;D-(-)fructose:(NADP+) 5-oxidoreductase;fructose 5-dehydrogenase (NADP+) Class Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname D-fructose:NADP+ 5-oxidoreductase Reaction(IUBMB) D-fructose + NADP+ = 5-dehydro-D-fructose + NADPH…

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KEGG ENZYME: 1.7.2.7

Entry EC 1.7.2.7                  Enzyme                                  Name Class Oxidoreductases;Acting on other nitrogenous compounds as donors;With a cytochrome as acceptorBRITE hierarchy Sysname hydrazine:ferricytochrome-c oxidoreductase Reaction(IUBMB) hydrazine + H2O + 3 ferricytochrome c = nitric oxide + ammonium + 3 ferrocytochrome c [RN:R09799] Reaction(KEGG) Substrate Product nitric oxide [CPD:C00533]; ammonium; ferrocytochrome c [CPD:C00126] Comment The enzyme,…

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kegg IDs to pathways in R

kegg IDs to pathways in R 0 Hi all, I have never done this before but i suspect there must be an easy way to convert KEGG ids to pathways in R. I have a dataframe containing info from 1000 sth bacterial genomes; their taxonomy, their orfs and the kegg…

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KEGG ENZYME: 1.1.3.39

KEGG ENZYME: 1.1.3.39     ENZYME: 1.1.3.39 Help Entry EC 1.1.3.39                 Enzyme                                  Name nucleoside oxidase (H2O2-forming) Class Oxidoreductases;Acting on the CH-OH group of donors;With oxygen as acceptorBRITE hierarchy Sysname nucleoside:oxygen 5′-oxidoreductase (H2O2-forming) Reaction(IUBMB) adenosine + 2 O2 + H2O = 9-riburonosyladenine + 2 H2O2 (overall reaction) [RN:R05695]; (1a) adenosine + O2 = 5′-dehydroadenosine…

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KEGG ENZYME: 2.1.4.1

Entry EC 2.1.4.1                  Enzyme                                  Name glycine amidinotransferase;arginine-glycine amidinotransferase;arginine-glycine transamidinase;glycine transamidinase Class Transferases;Transferring one-carbon groups;AmidinotransferasesBRITE hierarchy Sysname L-arginine:glycine amidinotransferase Reaction(IUBMB) L-arginine + glycine = L-ornithine + guanidinoacetate [RN:R00565] Reaction(KEGG) Substrate Product Comment Canavanine can act instead of arginine. History EC 2.1.4.1 created 1961 as EC 2.6.2.1, transferred 1965 to EC 2.1.4.1 Pathway ec00260  …

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KEGG ENZYME: 1.4.1.4

Entry EC 1.4.1.4                  Enzyme                                  Name glutamate dehydrogenase (NADP+);glutamic dehydrogenase;dehydrogenase, glutamate (nicotinamide adenine dinucleotide (phosphate));glutamic acid dehydrogenase;L-glutamate dehydrogenase;L-glutamic acid dehydrogenase;NAD(P)+-glutamate dehydrogenase;NAD(P)H-dependent glutamate dehydrogenase;glutamate dehydrogenase (NADP+) Class Oxidoreductases;Acting on the CH-NH2 group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname L-glutamate:NADP+ oxidoreductase (deaminating) Reaction(IUBMB) L-glutamate + H2O + NADP+ = 2-oxoglutarate + NH3…

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KEGG ENZYME: 2.5.1.84

Entry EC 2.5.1.84                 Enzyme                                  Name all-trans-nonaprenyl diphosphate synthase [geranyl-diphosphate specific];nonaprenyl diphosphate synthase (ambiguous);solanesyl diphosphate synthase (ambiguous);SolPP synthase (ambiguous);SPP-synthase (ambiguous);SPP synthase (ambiguous);solanesyl-diphosphate synthase (ambiguous);OsSPS2 Class Transferases;Transferring alkyl or aryl groups, other than methyl groups;Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)BRITE hierarchy Sysname geranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 7…

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Practical value of bits and SW-score in KEGG

Practical value of bits and SW-score in KEGG 1 Hello, Can someone explain to me the practical value of bits and SW-score in KEGG? What does it actually mean for my sequence? The image below shows paralogs table as shown in the base what is the practical value of these…

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Pathway enrichment analysis

Pathway enrichment analysis 1 Hi! I have found DEGs. What do I use for the pathway enrichment analysis; all DEGs or separate between up and down? Also is it normal to only choose a subset like the top 50 up-reg genes or would I like to take all the up-reg…

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KEGG ENZYME: 3.5.1.12

Entry EC 3.5.1.12                 Enzyme                                  Name biotinidase;amidohydrolase biotinidase Class Hydrolases;Acting on carbon-nitrogen bonds, other than peptide bonds;In linear amidesBRITE hierarchy Sysname biotin-amide amidohydrolase Reaction(IUBMB) biotin amide + H2O = biotin + NH3 [RN:R01076] Reaction(KEGG) Substrate Product Comment Also acts on biotin esters. History EC 3.5.1.12 created 1961 Pathway Orthology Genes  » show allTaxonomy…

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ANGPTL8/betatrophin improves glucose tolerance | DMSO

Introduction Insulin resistance is a major risk factor for metabolic syndrome (MetS), including type 2 diabetes mellitus (T2DM).1 T2DM is characterized by insulin resistance in the liver.2 Insulin resistance is an abnormal physiological state that occurs when cells are unable to use insulin effectively, leading to T2DM, a major health…

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How to get a list of all KEGG ko terms vs names?

How to get a list of all KEGG ko terms vs names? 2 I want to map a list of KEGG terms with their corresponding names. Is it possible to get a list of all KEGG terms and their descriptions/names? kegg annotation rna-seq • 1.0k views Hi. I am not…

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KEGG COMPOUND: C01771

KEGG COMPOUND: C01771     COMPOUND: C01771 Help Entry C01771                      Compound                                Name 2-Butenoate;2-Butenoic acid;Crotonic acid;3-Methylacrylic acid Formula C4H6O2 Exact mass 86.0368 Mol weight 86.0892 Structure Mol fileKCF fileDB search Reaction Enzyme Other DBs KCF data Show ATOM        6            1   C2b C    22.1306  -15.0946            2   C6a C    23.3400  -15.7959            3   C2b C    20.9148  -15.7959            4   O6a O    23.3400  -17.4782            5   O6a O    24.5495  -15.0946            6   C1a C    19.7053  -15.0946BOND        5            1     1   2 1            2     1   3 2            3     2   4 1            4     2   5 2            5     3   6 1 » Japanese version DBGET…

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